Taxonomic chauvinism revisited: insight from parental care research

Parental care (any non-genetic contribution by a parent that appears likely to increase the fitness of its offspring) is a widespread trait exhibited by a broad range of animal taxa. In addition to influencing the fitness of parent(s) and offspring, parental care may be inextricably involved in other evolutionary processes, such as sexual selection and the evolution of endothermy. Yet, recent work has demonstrated that bias related to taxonomy is prevalent across many biological disciplines, and research in parental care may be similarly burdened. Thus, I used parental care articles published in six leading journals of fundamental behavioral sciences (Animal Behaviour, Behavioral Ecology, Behavioral Ecology and Sociobiology, Ethology, Hormones and Behavior, and Physiology & Behavior) from 2001–2010 (n = 712) to examine the year-to-year dynamics of two types of bias related to taxonomy across animals: (1) taxonomic bias, which exists when research output is not proportional to the frequency of organisms in nature, and (2) taxonomic citation bias, which is a proxy for the breadth of a given article—specifically, the proportion of articles cited that refer solely to the studied taxon. I demonstrate that research on birds likely represents a disproportionate amount of parental care research and, thus, exhibits taxonomic bias. Parental care research on birds and mammals also refers to a relatively narrow range of taxonomic groups when discussing its context and, thus, exhibits taxonomic citation bias. Further, the levels of taxonomic bias and taxonomic citation bias have not declined over the past decade despite cautionary messages about similar bias in related disciplines— in fact, taxonomic bias may have increased. As in Bonnet et al. (2002), my results should not be interpreted as evidence of an ‘ornithological Mafia’ conspiring to suppress other taxonomic groups. Rather, I generate several rational hypotheses to determine why bias persists and to guide future work.     

Can Research Assessments Themselves Cause Bias in Behaviour Change Trials? A Systematic Review of Evidence from Solomon 4-Group Studies

Background

The possible effects of research assessments on participant behaviour have attracted research interest, especially in studies with behavioural interventions and/or outcomes. Assessments may introduce bias in randomised controlled trials by altering receptivity to intervention in experimental groups and differentially impacting on the behaviour of control groups. In a Solomon 4-group design, participants are randomly allocated to one of four arms: (1) assessed experimental group; (2) unassessed experimental group (3) assessed control group; or (4) unassessed control group. This design provides a test of the internal validity of effect sizes obtained in conventional two-group trials by controlling for the effects of baseline assessment, and assessing interactions between the intervention and baseline assessment. The aim of this systematic review is to evaluate evidence from Solomon 4-group studies with behavioural outcomes that baseline research assessments themselves can introduce bias into trials.

Methodology/Principal Findings

Electronic databases were searched, supplemented by citation searching. Studies were eligible if they reported appropriately analysed results in peer-reviewed journals and used Solomon 4-group designs in non-laboratory settings with behavioural outcome measures and sample sizes of 20 per group or greater. Ten studies from a range of applied areas were included. There was inconsistent evidence of main effects of assessment, sparse evidence of interactions with behavioural interventions, and a lack of convincing data in relation to the research question for this review.

Conclusions/Significance

There were too few high quality completed studies to infer conclusively that biases stemming from baseline research assessments do or do not exist. There is, therefore a need for new rigorous Solomon 4-group studies that are purposively designed to evaluate the potential for research assessments to cause bias in behaviour change trials.     

Systematics of the Soft-plumaged Petrel Pterodroma mollis (Procellariidae): new insight from the study of vocalizations

The taxonomic status of the populations of the polytypic Soft-plumaged Petrel Pterodroma mollis is controversial. Previous taxonomic studies used morphological characters (measurements and colouration) and univariate statistics. In this study, I add the use of multivariate statistics on morphological (biometry and colouration) and behavioural characters (vocalizations) of the petrels. Vocalizations are especially relevant in nocturnal burrowing petrels (such as the Soft-plumaged Petrel) and act as behavioural isolating mechanisms. The analysis, based on 535 calls from seven of the 11 known breeding localities of the species, showed that physical parameters of the call did not overlap at all between breeding localities in the northern and southern hemispheres but did so within each hemisphere. Conversely, the morphological analysis, based on morphometries from ten localities, displayed wide and significant intra-hemisphere variation, whereas there was no consistent difference between northern and southern parts of the breeding range. Thus analysis of the two sets of characters gave contradictory results. Calls, owing to their role in species-specific recognition in these birds, should be given priority over other characters for species separation. I suggest that only two species should be recognized, Pterodroma mollis and Pterodroma feae, with three subspecies each. I also examined behavioural affinities between P. mollislfeae groups and other gadfly petrels and found that P. mollis/feae were closest to Pterodroma cahow, whilst Pterodroma hasitata on the one hand and Pterodroma phaeopygia and Pterodroma externa (which may comprise two species instead of one) on the other belong to other groups of gadfly petrels.     

Towards objectivity in research evaluation using bibliometric indicators – A protocol for incorporating complexity

Publications are thought to be an integrative indicator best suited to measure the multifaceted nature of scientific performance. Therefore, indicators based on the publication record (citation analysis) are the primary tool for rapid evaluation of scientific performance. Nevertheless, it has to be questioned whether the indicators really do measure what they are intended to measure because people adjust to the indicator value system by optimizing their indicator rather than their performance. Thus, no matter how sophisticated an indicator may be, it will never be proof against manipulation. A literature review identifies the most critical problems of citation analysis: database-related problems, inflated citation records, bias in citation rates and crediting of multi-author papers. We present a step-by-step protocol to address these problems. By applying this protocol, reviewers can avoid most of the pitfalls associated with the pure numbers of indicators and achieve a fast but fair evaluation of a scientist's performance. We as ecologists should accept complexity not only in our research but also in our research evaluation and should encourage scientists of other disciplines to do so as well.     

Dissemination biases in ecology: effect sizes matter more than quality

Publication and citation decisions in ecology are likely influenced by many factors, potentially including journal impact factors, direction and magnitude of reported effects, and year of publication. Dissemination bias exists when publication or citation of a study depends on any of these factors. We defined several dissemination biases and determined their prevalence across many sub‐disciplines in ecology, then determined whether or not data quality also affected these biases. We identified dissemination biases in ecology by conducting a meta‐analysis of citation trends for 3867 studies included in 52 meta‐analyses. We correlated effect size, year of publication, impact factor and citation rate within each meta‐analysis. In addition, we explored how data quality as defined in meta‐analyses (sample size or variance) influenced each form of bias. We also explored how the direction of the predicted or observed effect, and the research field, influenced any biases. Year of publication did not influence citation rates. The first papers published in an area reported the strongest effects, and high impact factor journals published the most extreme effects. Effect size was more important than data quality for many publication and citation trends. Dissemination biases appear common in ecology, and although their magnitude was generally small many were associated with theory tenacity, evidenced as tendencies to cite papers that most strongly support our ideas. The consequences of this behavior are amplified by the fact that papers reporting strong effects were often of lower data quality than papers reporting much weaker effects. Furthermore, high impact factor journals published the strongest effects, generally in the absence of any correlation with data quality. Increasing awareness of the prevalence of theory tenacity, confirmation bias, and the inattention to data quality among ecologists is a first step towards reducing the impact of these biases on research in our field.     

Dactylogyridae 2022: a meta-analysis of phylogenetic studies and generic diagnoses of parasitic flatworms using published genetic and morphological data

Dactylogyridae is one of the most studied families of parasitic flatworms with more than 1000 species and 166 genera described to date including ecto- and endoparasites. Dactylogyrid monogeneans were suggested as model organisms for host-parasite macroevolutionary and biogeographical studies due to the scientific and economic importance of some of their host lineages. Consequently, an array of phylogenetic research into different dactylogyrid lineages has been produced over the past years but the last family-wide study was published 16 years ago. Here, we provide a meta-analysis of the phylogenetic relationships of Dactylogyridae including representatives of all genera with available molecular data (n = 67). First, we investigate the systematic informativeness of morphological characters widely used to diagnose dactylogyrid genera through a parsimony analysis of the characters, character mapping, and phylogenetic comparative methods. Second, we provide an overview of the current state of the systematics of the family and its subfamilies, and summarise potentially poly- and paraphyletic genera. Third, we elaborate on the implications of taxonomic, citation, and confirmation bias in past studies. Fourth, we discuss host range, biogeographical, and freshwater-marine patterns. We found two well-supported macroclades which we assigned to the subfamilies Dactylogyrinae and Ancyrocephalinae. These subfamilies further include 16 well-supported clades with only a few synapomorphies that could be deduced from generic diagnoses in the literature. Furthermore, few morphological characters considered systematically informative at the genus level display a strong phylogenetic signal. However, the parsimony analysis suggests that these characters provide little information on the relationships between genera. We conclude that a strong taxonomic bias and low coverage of DNA sequences and regions limit knowledge on morphological and biogeographical evolutionary patterns that can be inferred from these results. We propose addressing potential citation and confirmation biases through a ‘level playing field’ multiple sequence alignment as provided by this study.     

Flawed citation practices facilitate the unsubstantiated perception of a global trend toward increased jellyfish blooms

Speculation over a global rise in jellyfish populations has become widespread in the scientific literature, but until recently the purported ‘global increase’ had not been tested. Here we present a citation analysis of peer‐reviewed literature to track the evolution of the current perception of increases in jellyfish and identify key papers involved in its establishment. Trend statements and citation threads were reviewed and arranged in a citation network. Trend statements were assessed according their degree of affirmation and spatial scale, and the appropriateness of the citations used to support statements was assessed. Analyses showed that 48.9% of publications misinterpreted the conclusions of cited sources, with a bias towards claiming jellyfish populations are increasing, with a single review having the most influence on the network. Collectively, these disparities resulted in a network based on unsubstantiated statements and citation threads. As a community, we must ensure our statements about scientific findings in general are accurately substantiated and carefully communicated such that incorrect perceptions, as in the case of jellyfish blooms, do not develop in the absence of rigorous testing.     

Cladistic Analysis of Human Evolution: Some Points on Character Selection

Cladistic analysis strongly depends on accurate character choice. Usually, characters include morphology or molecules, but other sources of evidence are also employed. These include stratigraphic ages of taxa and behavioural data. The inclusion of time is a controversial issue, which has no Darwinian basis. However, the cladistic treatment of stratigraphic age has the potential to resolve problematic phylogenies. Here, it is proposed that the use of stratigraphic data in phylogenetic inference should be seen as a temporary shortcut, to resolve complex phylogenies in the wait for new character and taxonomic samplings, because phylogenetic hypotheses should be based on biological evidence only. Archaeologists working on toolmaking can provide behavioural data in human prehistory. In fact, while a tool itself is not biological evidence, the movements of hands and arms needed to prepare it are biological evidence and can be compared and scored for cladistic analysis. Such an approach has been formalized in studies on functional morphology of some vertebrates. The taxonomic data set to be used in cladistic analysis should include as many taxa as possible, and also very incomplete specimens should be used. In many cases, incomplete specimens had the potential to resolve complex phylogenies by adding new character combinations that cannot be scored in molecule-based phylogenetic studies.     

A simulation test of Smith's “degrees of freedom” correction for comparative studies

Computer simulation was used to test Smith's (1994) correction for phylogenetic nonindependence in comparative studies. Smith's method finds effective N, which is computed using nested analysis of variance, and uses this value in place of observed N as the baseline degrees of freedom (df) for calculating statistical significance levels. If Smith's formula finds the correct df, distributions of computer-generated statistics from simulations with observed N nonindependent species should match theoretical distributions (from statistical tables) with the df based on effective N. The computer program developed to test Smith's method simulates character evolution down user-specified phylogenies. Parameters were systematically varied to discover their effects on Smith's method. In simulations in which the phylogeny and taxonomy were identical (tests of narrow-sense validity), Smith's method always gave conservative statistical results when the taxonomy had fewer than five levels. This conservative departure gave way to a liberal deviation in type I error rates in simulations using more than five taxonomic levels, except when species values were nearly independent. Reducing the number of taxonomic levels used in the analysis, and thereby eliminating available information regarding evolutionary relationships, also increased type I error rates (broad-sense validity), indicating that this may be inappropriate under conditions shown to have high type I error rates. However, the use of taxonomic categories over more accurate phylogenies did not create a liberal bias in all cases in the analysis performed here. The effect of correlated trait evolution was ambiguous but, relative to other parameters, negligible. © 1995 Wiley-Liss, Inc.     

Optimal behaviour can violate the principle of regularity

Understanding decisions is a fundamental aim of behavioural ecology, psychology and economics. The regularity axiom of utility theory holds that a preference between options should be maintained when other options are made available. Empirical studies have shown that animals violate regularity but this has not been understood from a theoretical perspective, such decisions have therefore been labelled as irrational. Here, I use models of state-dependent behaviour to demonstrate that choices can violate regularity even when behavioural strategies are optimal. I also show that the range of conditions over which regularity should be violated can be larger when options do not always persist into the future. Consequently, utility theory—based on axioms, including transitivity, regularity and the independence of irrelevant alternatives—is undermined, because even alternatives that are never chosen by an animal (in its current state) can be relevant to a decision.     

Coordinating the traditional and modern approaches in the systematics of insects

The problem of coordinating the traditional and modern approaches to systematics is ever-lasting due to the continuous development and enrichment of our knowledge of biodiversity, means of analysis, and concepts. Comparative morphology was and still is the cornerstone of studies of insect taxonomy. It gives the most extensive and diverse information on the organisms studied, particularly when it is supported by the data on embryology and functional morphology as well as by analysis of adaptive significance of morphological characters. The limitations of this approach are often related to the presence of homoplasies, reversions, etc. Comparative paleontology is the only approach providing direct evidence of the historical succession of taxa and their characters. However, this approach is fully applicable only to some groups due to the specific features of their morphology and taphonomy. All the modern approaches (molecular, cytogenetic, etc.) are very informative but also have their own limitations; they should not be contrasted with the traditional approaches and certainly should not replace them. The traditional approaches do not become obsolete; it is only their comparative importance in the set of taxonomic tools that may be reevaluated. No single approach can be considered universal for an unambiguous reconstruction of phylogeny and substantiation of the natural system of taxa. Each approach has its own advantages and limitations, and only combined use of different approaches allows a broader range of the problems to be solved. Different approaches may prevail in the studies of different groups of insects and at different levels of taxonomic hierarchy. The intuition of the taxonomist, which is so often criticized by the followers of “objective” systematics, is based on taxonomic experience and scope of knowledge of a particular taxon. It does not imply a subjective bias, but allows the taxonomist to choose the instruments adequate to a particular case.     

To change or not to change experimenters: caveats for repeated behavioural and physiological measures in Montagu's harrier

Animals facing anthropogenic disturbances may exhibit different anti‐predator responses depending on their perception of the risk. Experimental measures of behavioural and physiological traits may be impacted by the disturbance due to experimenter handlings and activities. In this study, we assessed the behavioural and physiological responses of Montagu's harrier chicks Circus pygargus from 14 nests, visited four times from hatching to fledgling by either the same (group I) or different (group NI) experimenters. Escape, aggressiveness and stress‐induced corticosterone concentration increased for both groups over time but chicks from group I showed a higher increase in their behavioural and physiological responses than chicks from group NI. This increase occurred after the second visit when experimenters took the first blood sampling on nestlings. Handling by the same experimenters throughout the study did not result in habituation but in sensitization. Our results suggest that Montagu's harrier nestlings may discriminate between the people who visit their nest and respond to experimenters’ identity. Therefore, we urge researchers working on behaviour and/or the physiology of stress including repeated measurements (such as animal personality studies for instance) to consider whether the experiments should or should not be conducted by the same experimenters (as usually done to minimize bias) as it can influence the outcomes of the experiments.     

Behavioural and ecological correlates of natural hybridization in birds

Hybridization and speciation are central to evolutionary biology. Although birds have been studied more thoroughly than any other vertebrate class, there have still been few macro-evolutionary analyses. Here, I present results based on 65 phylogenetically independent hybrid types from the western Palearctic, focusing on behavioural and ecological correlates of hybridization. The main results are as follows. (1) Hybrids that are easier to detect were more often reported. (2) A positive correlation exists between population size (mean of both parent species) and the number of hybrids. After accounting for these confounding variables in a General Linear Model, I found (3) that sympatric species pairs produced fewer hybrids than did parapatric species pairs and (4) pairs with at least one of the parent species reported as endangered produced a greater number of hybrids whereas (5) species pairs with high male parental (paternal) care produced fewer hybrids. Other variables were excluded by a stepwise procedure in the following order: sexual dichromatism; body weight differences; publication bias. Phylogenetic information was available for a small number of hybrids but did not influence the results.     

Perceptual and Gaze Biases during Face Processing: Related or Not?

Previous studies have demonstrated a left perceptual bias while looking at faces, due to the fact that observers mainly use information from the left side of a face (from the observer''s point of view) to perform a judgment task. Such a bias is consistent with the right hemisphere dominance for face processing and has sometimes been linked to a left gaze bias, i.e. more and/or longer fixations on the left side of the face. Here, we recorded eye-movements, in two different experiments during a gender judgment task, using normal and chimeric faces which were presented above, below, right or left to the central fixation point or on it (central position). Participants performed the judgment task by remaining fixated on the fixation point or after executing several saccades (up to three). A left perceptual bias was not systematically found as it depended on the number of allowed saccades and face position. Moreover, the gaze bias clearly depended on the face position as the initial fixation was guided by face position and landed on the closest half-face, toward the center of gravity of the face. The analysis of the subsequent fixations revealed that observers move their eyes from one side to the other. More importantly, no apparent link between gaze and perceptual biases was found here. This implies that we do not look necessarily toward the side of the face that we use to make a gender judgment task. Despite the fact that these results may be limited by the absence of perceptual and gaze biases in some conditions, we emphasized the inter-individual differences observed in terms of perceptual bias, hinting at the importance of performing individual analysis and drawing attention to the influence of the method used to study this bias.     

Island ecology and contingent theory: the role of spatial scale and taxonomic bias

Scale, the scale dependency of patterns and processes, and the ways that organisms scale their responses to these patterns and processes are central to island and landscape ecology. Here, we take a database of studies in island ecology and investigate how studies have changed over a 40-year period with respect to spatial scale and organisms studied. We demonstrate that there have been changes in the spatial scale of islands studied and that there is taxonomic bias in favour of vertebrates in island ecological studies when compared to scientific publications as a whole. We discuss how such taxonomic bias may have arisen and discuss the implications for ecology and biogeography.     

Genome-wide codon usage profiling of ocular infective Chlamydia trachomatis serovars and drug target identification

Chlamydia trachomatis (C.t) is a Gram-negative obligate intracellular bacteria and is a major causative of infectious blindness and sexually transmitted diseases. Among the varied serovars of this organism, A, B and C are reported as prominent ocular pathogens. Genomic studies of these strains shall aid in deciphering potential drug targets and genomic influence on pathogenesis. Hence, in this study we performed deep statistical profiling of codon usage in these serovars. The overall base composition analysis reveals that these serovars are over biased to AU than GC. Similarly, relative synonymous codon usage also showed preference towards A/U ending codons. Parity Rule 2 analysis inferred unequal distribution of AT and GC, indicative of other unknown factors acting along with mutational pressure to influence codon usage bias (CUB). Moreover, absolute quantification of CUB also revealed lower bias across these serovars. The effect of natural selection on CUB was also confirmed by neutrality plot, reinforcing natural selection under mutational pressure turned to be a pivotal role in shaping the CUB in the strains studied. Correspondence analysis (COA) clarified that, C.t C/TW-3 to show a unique trend in codon usage variation. Host influence analysis on shaping the codon usage pattern also inferred some speculative relativity. In a nutshell, our finding suggests that mutational pressure is the dominating factor in shaping CUB in the strains studied, followed by natural selection. We also propose potential drug targets based on cumulative analysis of strand bias, CUB and human non-homologue screening.     

Future directions in behavioural syndromes research

A behavioural syndrome occurs when individuals behave in a consistent way through time or across contexts and is analogous to 'personality' or 'temperament'. Interest is accumulating in behavioural syndromes owing to their important ecological and evolutionary consequences. There are plenty of opportunities in this burgeoning young field to integrate proximate and functional approaches to studying behaviour, but there are few guidelines about where to start or how to design a study on behavioural syndromes. After summarizing what we do and do not know, this brief review aims to act as a general guide for studying behavioural syndromes. Although the array of possible behavioural combinations can seem overwhelming, there are at least four different strategies that can be used to choose which behaviours or contexts to study in a behavioural syndromes view. I describe the strengths and weaknesses of these non-exclusive strategies, and then discuss the methodological and statistical issues raised by such studies.     

Relative brain size and ecology in birds

We test the hypothesis that the relative sizes of the different parts of the brain (brain stem, optic lobes, cerebellum and cerebral hemispheres), measured after body size effects have been removed, are associated with differences in behaviour and ecology across bird species.
The results demonstrate that behavioural and ecological correlates of relative brain size are not independent of each other. When the effects of variation in other categories are accounted for, the strongest single effect is due to relatively large brain sizes being associated with altricial development. It is unlikely that this effect is due to the confounding influence of taxonomic associations.
Overall, the results do not provide support for the idea that differences in measures of environmental complexity select for differences in relative brain size.     

以演化时间为新增指标构建真菌分类系统

随着分子系统发育研究的普及,真菌各分类类群逐渐被修订为单系发生类群,通常结合形态学特征为代表的表型特征("单系+表型特征")对不同的分类等级命名是最为普遍的方法.历史上存在的大量多系名称被逐步修订、补充和完善,各个不同等级类群的分类系统变得更加合理、客观和趋于自然,这是分类学进程中巨大的进步.然而系统发育重建所揭示的单...     

OF MICE AND KIN: THE FUNCTIONAL SIGNIFICANCE OF KIN BIAS IN SOCIAL BEHAVIOUR

1. Sharing recent ancestry (kinship) increases the degree of genetic similarity between individuals, where genetic similarity could mean anything from sharing a particular allele to sharing an entire genome. 2. Genetic similarity can influence behavioural and other responses between individuals in a number of ways, discriminatory and non-discriminatory. All are likely to result in kin bias, because of the correlation between genetic similarity and kinship, but only some should be regarded as involving kin discrimination. 3. Non-discriminatory kin bias could arise through close relatives sharing, for instance, physical characteristics (such as those influencing competitive ability), thresholds of behavioural response or requirements for particular resources. 4. Discriminatory kin bias could arise through the direct perception of genetic similarity between individuals (direct similarity discrimination) or the use of cues likely to correlate with genetic similarity (indirect similarity discrimination--of which kin discrimination is one form). Alternatively, it could arise incidentally through mistaken identity or discrimination at some other level, such as species identification. 5. Experiments with laboratory and wild house mice have revealed kin bias in a number of contexts, including (a) parental and infanticidal behaviour, (b) sexual development and behaviour and (c) investigatory behaviour and passive body contact among juveniles and adults. 6. While kin bias in mice has been interpreted as evidence for kin discrimination, there are several problems with such an interpretation. These include (a) pronounced and complex effects of familiarity on discrimination, (b) a high risk of error-proneness in the indirect cues used in apparent kin discrimination and (c) weak and easily disrupted kin bias effects in certain contexts. 7. Consideration of social structure and discriminatory responses within populations of wild house mice leads to an alternative explanation for some kin bias in terms of incidental discrimination based on social group membership. 8. Several results from laboratory experiments suggest incidental discrimination is a more parsimonious explanation than kin discrimination for some intrasexual kin bias in behaviour. However, kin or direct similarity discrimination appears to be the most likely explanation for other aspects of intrasexual kin bias and for intersexual kin bias.